src/jalview/io/WSWUBlastClient.java

   1 package jalview.io;\r
   2 \r
   3 import org.apache.axis.client.*;\r
   4 import javax.xml.namespace.QName;\r
   5 import java.util.*;\r
   6 import jalview.datamodel.*;\r
   7 import jalview.gui.*;\r
   8 import javax.swing.*;\r
   9 import java.util.*;\r
  10 import java.awt.*;\r
  11 \r
  12 public class WSWUBlastClient\r
  13 {\r
  14   JInternalFrame outputFrame = new JInternalFrame();\r
  15   CutAndPasteTransfer output = new CutAndPasteTransfer();\r
  16   int jobsRunning = 0;\r
  17 \r
  18   public WSWUBlastClient(AlignmentI al, ArrayList ids)\r
  19   {\r
  20     outputFrame.setContentPane(output);\r
  21     output.setText("To display sequence features an exact Uniprot id with 100% sequence identity match must be entered."\r
  22                 +"\nIn order to display these features, try changing the names of your sequences to the ids suggested below.");\r
  23     Desktop.addInternalFrame(outputFrame, "BLASTing for unidentified sequences ", 800,300);\r
  24 \r
  25     for(int i=0; i<ids.size(); i++)\r
  26     {\r
  27      SequenceI sequence =  al.findName( ids.get(i).toString() );\r
  28      StringBuffer nonGapped = new StringBuffer();\r
  29       for (int n = 0; n < sequence.getSequence().length(); n++)\r
  30       {\r
  31         if (!jalview.util.Comparison.isGap(sequence.getCharAt(n)))\r
  32           nonGapped.append(sequence.getCharAt(n));\r
  33       }\r
  34 \r
  35      BlastThread thread = new BlastThread(ids.get(i).toString(),  nonGapped.toString());\r
  36      thread.start();\r
  37      jobsRunning ++;\r
  38      }\r
  39      ImageTwirler thread = new ImageTwirler();\r
  40      thread.start();\r
  41   }\r
  42 \r
  43   class ImageTwirler extends Thread\r
  44   {\r
  45     ImageIcon [] imageIcon;\r
  46     int imageIndex = 0;\r
  47     public ImageTwirler()\r
  48     {\r
  49       imageIcon = new ImageIcon[9];\r
  50       for(int i=0; i<9; i++)\r
  51       {\r
  52         java.net.URL url = getClass().getResource("/images/dna" + (i+1) + ".gif");\r
  53         if (url != null)\r
  54           imageIcon[i] = new ImageIcon(url);\r
  55       }\r
  56     }\r
  57 \r
  58     public void run()\r
  59     {\r
  60       while(jobsRunning>0)\r
  61       {\r
  62         try{\r
  63           Thread.sleep(100);\r
  64           imageIndex++;\r
  65           imageIndex %=9;\r
  66           outputFrame.setFrameIcon( imageIcon[imageIndex]);\r
  67           outputFrame.setTitle("BLASTing for unidentified sequences - "+jobsRunning+" jobs running.");\r
  68 \r
  69         }catch(Exception ex){}\r
  70 \r
  71       }\r
  72     }\r
  73   }\r
  74 \r
  75 \r
  76 \r
  77 \r
  78   class BlastThread extends Thread\r
  79   {\r
  80     String sequence;\r
  81     String seqid;\r
  82     String jobid;\r
  83     boolean jobComplete = false;\r
  84 \r
  85     BlastThread(String id, String sequence)\r
  86     {\r
  87       this.sequence = sequence;\r
  88       seqid = id;\r
  89     }\r
  90 \r
  91     public void run()\r
  92     {\r
  93       StartJob();\r
  94 \r
  95       while (!jobComplete)\r
  96       {\r
  97         try\r
  98         {\r
  99           Call call = (Call)new Service().createCall();\r
 100           call.setTargetEndpointAddress(new java.net.URL(\r
 101               "http://www.ebi.ac.uk/cgi-bin/webservices/WSWUBlast"));\r
 102           call.setOperationName(new QName("WSWUBlast", "polljob"));\r
 103           String result = (String) call.invoke(new Object[]\r
 104                                                {jobid, "xml"});\r
 105           if(result.indexOf("JOB PENDING")==-1 && result.indexOf("JOB RUNNING")==-1)\r
 106           {\r
 107                 parseResult(seqid, result);\r
 108                 jobComplete = true;\r
 109                 jobsRunning --;\r
 110           }\r
 111           Thread.sleep(5000);\r
 112           // System.out.println("WSWuBlastClient: I'm alive "+seqid+" "+jobid); // log.debug\r
 113         }\r
 114         catch (Exception ex)\r
 115         {}\r
 116       }\r
 117     }\r
 118 \r
 119     void StartJob()\r
 120     {\r
 121       HashMap params = new HashMap();\r
 122       params.put("database", "uniprot");\r
 123       params.put("sensitivity", "low");\r
 124       params.put("sort", "totalscore");\r
 125       params.put("matrix", "pam10");\r
 126       params.put("program", "blastp");\r
 127       params.put("alignments", "5");\r
 128       params.put("outformat", "xml");\r
 129       params.put("searchtype", "1");\r
 130       byte[] seqbytes = sequence.getBytes();\r
 131 \r
 132       try\r
 133       {\r
 134         Call call = (Call)new Service().createCall();\r
 135         call.setTargetEndpointAddress(new java.net.URL(\r
 136             "http://www.ebi.ac.uk/cgi-bin/webservices/WSWUBlast"));\r
 137         call.setOperationName(new QName("WSWUBlast", "doWUBlast"));\r
 138         String result = (String) call.invoke(new Object[]\r
 139                                              {params, seqbytes});\r
 140         jobid = result;\r
 141         System.out.println("http://www.ebi.ac.uk/cgi-bin/webservices/WSWUBlast JobId '"+jobid+"'");\r
 142 \r
 143       }\r
 144       catch (Exception exp)\r
 145       {\r
 146         System.err.println("WSWUBlastClient error:\n" + exp.toString());\r
 147         exp.printStackTrace();\r
 148       }\r
 149     }\r
 150   }\r
 151 \r
 152     void parseResult(String id1, String res)\r
 153     {\r
 154       StringTokenizer st = new StringTokenizer(res, "\n");\r
 155       String data;\r
 156       String id2;\r
 157       int maxFound = 90;\r
 158       StringBuffer buffer = new StringBuffer("\n\n"+id1+" :");\r
 159 \r
 160       while( st.hasMoreTokens() )\r
 161       {\r
 162         data = st.nextToken();\r
 163 \r
 164         if(data.indexOf("database=\"uniprot\" id=")>-1)\r
 165         {\r
 166           int index =  data.indexOf("database=\"uniprot\" id=")+ 23;\r
 167           id2 = data.substring( index, data.indexOf("\"", index) );\r
 168           while( data.indexOf("</alignment>")==-1)\r
 169           {\r
 170             data = st.nextToken();\r
 171             if(data.indexOf("<identity>")>-1)\r
 172             {\r
 173               int value = Integer.parseInt( data.substring(data.indexOf("<identity>")+10, data.indexOf("</identity>")));\r
 174               if(value>=maxFound)\r
 175               {\r
 176                 maxFound = value;\r
 177                 buffer.append(" "+ id2 + " " + value+"%; ");\r
 178               }\r
 179             }\r
 180           }\r
 181 \r
 182         }\r
 183 \r
 184 \r
 185       }\r
 186 \r
 187       output.setText(output.getText()+buffer.toString());\r
 188     }\r
 189 \r
 190 }\r